> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/sv-annotation-thresholds.md).

# SV annotation thresholds

The Emedgene SV annotation pipeline integrates multiple structural variant databases, including allele frequency sources (e.g., gnomAD SV) and variant/region pathogenicity resources (e.g., ClinVar, ClinGen). Annotation is performed based on defined overlap thresholds tailored to the clinical significance of each database category

Present under Workbench & Pipeline in Organization Settings, this module enables configuration of annotation overlapping thresholds for structural variants with external and internal databases.

<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-21f5f5cd25fc68b74887b1009c76a7f7c2f949fd%2Fimage%20(39).png?alt=media" alt=""><figcaption><p>Organization settings > Workbench &#x26; Pipeline > SV annotation threshold</p></figcaption></figure>

{% hint style="info" %}
**Value Constraint**: Comprised between 0 to 1, with 2 decimals allowed.
{% endhint %}

### One Side Pathogenic <a href="#one-side-pathogenic" id="one-side-pathogenic"></a>

The One Side Pathogenic setting allows to set a threshold for identifying structural variants classified as pathogenic and likely pathogenic, such as those in ClinGen Pathogenic, ClinVar Pathogenic, DDDSyndromes, and Curate Pathogenic databases. It starts at a default of 0.7, and accepts value between 0 and 1.

### One Side Uncertain <a href="#one-side-uncertain" id="one-side-uncertain"></a>

The One Side Uncertain setting allows to set a threshold for identifying structural variants classified as uncertain, such as those in ClinGen VUS, ClinVar VUS, and Curate VUS databases. It starts at a default of 0.7, and accepts value between 0 and 1.

### Two Sided <a href="#two-sided" id="two-sided"></a>

The Two Sided setting allows to set a threshold for identifying structural variants classified as benign and likely benign, such as those in ClinGen Benign, ClinVar Benign, DECIPHER, DGV, gnomAD SV, 1000 genomes, and Curate Benign databases. It starts at a default of 0.7, and accepts value between 0 and 1.


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